[BlueObelisk-discuss] Looking for collaborators in Scala project

[Stefan Hoeck]

Dear all

I am an organic chemist at the Zurich University of Applied Sciences. A
couple of months ago we published an article in the Journal of
Cheminformatics about the beginnings of a purely functional cheminformatics
toolkit written in Scala (the article can be found here:
http://www.jcheminf.com/content/4/1/38/abstract). So far, this toolkit only
supports SMILES parsing and representing molecules in a basic, immutable
graph data structure. I am now looking for people interested in pushing
this project forward. The toolkit, which we called 'chemf', is open-source
(the source code is hosted on github: https://github.com/stefan-hoeck/chemf)
but it hasn't seen much activity lately since so far I have been the only
person working on it.

So, I am looking for people helping me implement the typical algorithms
needed for a fully fledged cheminformatics toolkit in a purely functional,
referentially transparent way. The algorithms may be implemented in an
imperative style in the background, but they need to be designed to work
with immutable data structures and produce such data structures as output.
I am aware that there are already quite a few cheminformtaics toolkits out
there, but to the best of my knowledge, those rich in functionality like
CDK or Open Babel provide algorithms that require mutable data structures
to work properly.

Note, that people wishing to contribute to this project do not necessarily
need to be able to write Scala code since if one sticks to Scala's
imperative side, Java source code can typically be transferred to Scala
source code quite easily.

Please excuse if this is not the right way or place to address the Blue
Obelisk community with such a request. Any help or input on this matter is
highly appreciated.

Best regards

Stefan Höck

[Peter Murray-Rust]

Post by Stefan Hoeck
Dear all
I am an organic chemist at the Zurich University of Applied Sciences. A
couple of months ago we published an article in the Journal of
Cheminformatics about the beginnings of a purely functional cheminformatics
http://www.jcheminf.com/content/4/1/38/abstract). So far, this toolkit
only supports SMILES parsing and representing molecules in a basic,
immutable graph data structure. I am now looking for people interested in
pushing this project forward. The toolkit, which we called 'chemf', is
https://github.com/stefan-hoeck/chemf) but it hasn't seen much activity
lately since so far I have been the only person working on it.

I am very interested in developing a Scala engine for CML - probably a cut
down version from the complete JUMBO6 . DaveMR (copied) has created a Scala
engine for MathML to integrate maths with chemistry.

Post by Stefan Hoeck
So, I am looking for people helping me implement the typical algorithms
needeam d for a fully fledged cheminformatics toolkit in a purely
functional, referentially transparent way. The algorithms may be
implemented in an imperative style in the background, but they need to be
designed to work with immutable data structures and produce such data
structures as output. I am aware that there are already quite a few
cheminformtaics toolkits out there, but to the best of my knowledge, those
rich in functionality like CDK or Open Babel provide algorithms that
require mutable data structures to work properly.

JUMBO has a wide range of tests so it should be possible to use them to
test the scala engine.

Post by Stefan Hoeck
Note, that people wishing to contribute to this project do not necessarily
need to be able to write Scala code since if one sticks to Scala's
imperative side, Java source code can typically be transferred to Scala
source code quite easily.

It will be very interesting to see how this works.

Post by Stefan Hoeck
Please excuse if this is not the right way or place to address the Blue
Obelisk community with such a request. Any help or input on this matter is
highly appreciated.
Absolutely the right place!